Difference between revisions of "Template:F5samples"
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− | {|style=" | + | {{Loading|loadingimage=sprites.gif}}<html> |
− | + | <style type="text/css" title="currentStyle"> | |
− | + | @import "/5/sstar/rb_js/html5button/datatables.css"; | |
− | + | @import "/5/sstar/rb_js/datatables/extras/TableTools/media/css/TableTools.css"; | |
− | + | </style> | |
− | + | <script type="text/javascript" src="/5/sstar/rb_js/jquery-1.7.1.min.js"></script> | |
− | + | <script type="text/javascript" src="/5/sstar/rb_js/html5button/datatables.js"></script> | |
− | + | <script type="text/javascript" src="/5/sstar/rb_js/custom/expoconvert.js"></script> | |
− | + | <script type="text/javascript" language="javascript" src="/5/sstar/rb_js/datatables/extras/TableTools/media/js/TableTools.min.js"></script> | |
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+ | </html>{{#outerfile_existance: /5/sstar/sstar_img/f5samples/riken_cellimg/{{PAGENAME}}.jpg |<html> | ||
+ | <div style="width:250px;height:250px;float:right;"><img width=250 src="/5/sstar/sstar_img/f5samples/riken_cellimg/</html>{{PAGENAME}}<html>.jpg"> | ||
+ | <div align="right">© RIKEN, 2013 <a href="http://creativecommons.org/licenses/by-sa/2.1/jp"><img src="/5/sstar/sstar_img/f5samples/riken_cellimg/by-sa_s.png" alt="by-sa"></a></div> | ||
+ | </div></html>}} | ||
+ | {{#set:id={{{id}}}}} | ||
+ | <table> | ||
+ | <tr><th scope="row" align="right">Name:</th><td>[[name::{{{name}}}]]</td></tr> | ||
+ | <tr><th scope="row" align="right">[[Property:Sample_species|Species]]:</th><td>[[sample_species::{{{sample_species}}}]]</td></tr> | ||
+ | <tr><th scope="row" align="right">[[Property:Library_accession_number|Library ID]]:</th><td>{{#replace:{{{library_id}}}|!|, }}</td></tr> | ||
+ | {{#ifexpr: {{#pos:{{{cagescan_library_id}}}|Cig}}|<tr><th scope="row" align="right">CAGEScan Library ID:</th><td>{{#replace:{{{cagescan_library_id}}}|!|, }}</td></tr>|}} | ||
+ | <tr><th scope="row" align="right">[[Property:Sample_category|Sample type]]:</th><td>{{{sample_category}}}</td></tr> | ||
+ | {{#ifeq: {{{sample_species}}} | Gallus gallus ||<tr><th scope="row" align="right">Genomic View:</th><td>{{#ifexpr: {{#pos:{{{zenbu_config}}}|ttp}}|[{{{zenbu_config}}} zenbu] |}} {{#ifeq: {{{sample_species}}} | Human (Homo sapiens) |[http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&tsCurTab=advancedTab&hgt_tsPage=&hgt_tSearch=search&tsName={{#replace:{{{id}}}|FF:|}} UCSC]| }}{{#ifeq: {{{sample_species}}} | Mouse (Mus musculus) |[http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&tsCurTab=advancedTab&hgt_tsPage=&hgt_tSearch=search&tsName={{#replace:{{{id}}}|FF:|}} UCSC]| }}</td></tr>}} | ||
+ | {{#ifexpr: {{#pos:{{{microRNAs_novel_cage}}}{{{microRNAs_novel_srna}}}|ttp}}| | ||
+ | {{#ifexpr: {{#pos:{{{microRNAs_novel_srna}}}|ttp}} | ||
+ | |{{#ifexpr: {{#pos:{{{microRNAs_novel_cage}}}|ttp}}|<tr><th scope="row" align="right">MicroRNAs:</th><td>Including candidate novel miRNAs<span style="font-size:xx-small;">([{{{microRNAs_novel_cage}}} CAGE samples], [{{{microRNAs_novel_srna}}} sRNA samples])</span><br/>Excluding candidate novel miRNAs<span style="font-size:xx-small;">([{{{microRNAs_nonnovel_cage}}} CAGE samples], [{{{microRNAs_nonnovel_srna}}} sRNA samples])</span></td></tr>|<tr><th scope="row" align="right">MicroRNAs:</th><td>Including candidate novel miRNAs<span style="font-size:xx-small;">([{{{microRNAs_novel_srna}}} sRNA samples])</span><br/>Excluding candidate novel miRNAs<span style="font-size:xx-small;">([{{{microRNAs_nonnovel_srna}}} sRNA samples])</span></td></tr>}} | ||
+ | |{{#ifexpr: {{#pos:{{{microRNAs_novel_cage}}}|ttp}}|<tr><th scope="row" align="right">MicroRNAs:</th><td>Including candidate novel miRNAs<span style="font-size:xx-small;">([{{{microRNAs_novel_cage}}} CAGE samples])</span><br/>Excluding candidate novel miRNAs<span style="font-size:xx-small;">([{{{microRNAs_nonnovel_cage}}} CAGE samples])</span></td></tr>|}} | ||
+ | }} | ||
+ | |}} | ||
+ | {{#ifexpr: {{#pos:{{{refex}}}|ttp}}| | ||
+ | <tr><th scope="row" align="right">RefEX:</th><td>[{{#replace:{{#replace:{{{refex}}}|[|%5b}}|]|%5d}} Specific genes] </td></tr>|}} | ||
+ | {{#ifexpr: {{#pos:{{{fantom_cat}}}|ttp}}| | ||
+ | <tr><th scope="row" align="right">FANTOM CAT:</th><td>{{ #vardefine: i | 1 }}{{#arraymap:{{{fantom_cat}}}|;;|$|[$ {{ #var: i }}{{ #vardefine: i | {{ #expr: {{ #var: i }} + 1 }} }}]|, }}</td></tr>|}} | ||
+ | {{#ifeq: {{{sample_species}}} | Human (Homo sapiens) | <tr><th scope="row" align="right">CAGEd-oPOSSUM:</th><td>[http://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM/results/precomputed/human/{{{id}}}/results.html link] </td></tr> | }}{{#ifeq: {{{sample_species}}} | Mouse (Mus musculus) | <tr><th scope="row" align="right">CAGEd-oPOSSUM:</th><td>[http://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM/results/precomputed/mouse/{{{id}}}/results.html link] </td></tr> | }}</table> | ||
+ | {|class="wikitable mw-collapsible mw-collapsed" style="width:auto" | ||
+ | ! Additional information | ||
|- | |- | ||
− | | | + | |<div style="width:50%; float:left;">Sample information<table cellspacing="0" border="1"> |
− | + | <tr><th>strain</th><td>{{#switch:{{{sample_strain}}}|,,,=NA| =NA |{{{sample_strain}}}}}</td></tr> | |
− | + | <tr><th>tissue</th><td>{{#switch:{{{sample_tissue}}}|,,,=NA| =NA |{{{sample_tissue}}}}}</td></tr> | |
− | | | + | <tr><th>dev stage</th><td>{{#switch:{{{sample_dev_stage}}}|,,,=NA| =NA |{{{sample_dev_stage}}}}}</td></tr> |
− | | | + | <tr><th>sex</th><td>{{#switch:{{{sample_sex}}}|,,,=NA| =NA |{{{sample_sex}}}}}</td></tr> |
− | + | <tr><th>age</th><td>{{#switch:{{{sample_age}}}|,,,=NA| =NA |{{{sample_age}}}}}</td></tr> | |
− | | | + | <tr><th>cell type</th><td>{{#switch:{{{sample_cell_type}}}|,,,=NA| =NA |{{{sample_cell_type}}}}}</td></tr> |
− | | | + | <tr><th>cell line</th><td>{{#switch:{{{sample_cell_line}}}|,,,=NA| =NA |{{{sample_cell_line}}}}}</td></tr> |
− | + | <tr><th>company</th><td>{{#switch:{{{sample_company}}}|,,,=NA| =NA |{{{sample_company}}}}}</td></tr> | |
− | | [ | + | <tr><th>collaboration</th><td>{{#switch:{{{sample_collaboration}}}|,,,=NA| =NA |{{{sample_collaboration}}}}}</td></tr> |
− | | | + | {{#if:{{{sample_info_link}}}|<tr><th style="background-color: #4169e1;">External link for information</th><td style="background-color: #f0f8ff;">[{{#explode:{{{sample_info_link}}}|;|-1}} {{#explode:{{{sample_info_link}}}|;|0}}]</td></tr>}}</table></div> |
− | + | <div style="width:50%; float:left;"> | |
− | | | + | RNA information<table cellspacing="0" border="1"> |
− | + | <tr><th>lot number</th><td>{{#switch:{{{rna_lot_number}}}|,,,=NA| =NA |{{{rna_lot_number}}}}}</td></tr> | |
− | + | <tr><th>catalog number</th><td>{{#switch:{{{rna_catalog_number}}}|,,,=NA| =NA |{{{rna_catalog_number}}}}}</td></tr> | |
− | | | + | <tr><th>sample type</th><td>{{#switch:{{{rna_sample_type}}}|,,,=NA| =NA |{{{rna_sample_type}}}}}</td></tr> |
− | | | + | <tr><th>extraction protocol <span style="background-color:white">[[Protocols:RNA_extraction|(Details)]]</span></th><td>{{#switch:{{{rna_extraction_protocol}}}|,,,=NA| =NA |{{{rna_extraction_protocol}}}}}</td></tr></table></div> |
− | + | |}{{#if:{{#pos:{{{DRA_sample_Accession}}}|@|0}}|{{DRAAccessionNumbers||{{{DRA_sample_Accession}}}|{{{accession_numbers}}}|{{{library_id}}}|{{{sample_species}}}}}|}}{{#vardefine:species_temp|{{#switch: {{{sample_species}}} | Human (Homo sapiens) = Hg19 | Mouse (Mus musculus) = Mm9 }}}}{{#switch: {{{sample_species}}} | |
− | | | + | |Human (Homo sapiens) = {{FastaBamfileCTSS||Hg19|{{{hg19fasta}}}||{{{hg19bam}}}|{{{hg19ctss}}}|Hg38|{{{hg38bam}}}|{{{hg38ctss}}}}} |
− | | | + | |Mouse (Mus musculus) = {{FastaBamfileCTSS||Mm9|{{{mm9fasta}}}||{{{mm9bam}}}|{{{mm9ctss}}}|Mm10|{{{mm10bam}}}|{{{mm10ctss}}}}} |
− | + | | | |
− | | | + | }}{{#if:{{#pos:{{{DRA_sample_Accession_HumanCAGEScan}}}|@|0}}|{{DRAAccessionNumbers|HumanCAGEScan|{{{DRA_sample_Accession_HumanCAGEScan}}}|{{{accession_numbers_HumanCAGEScan}}}|{{{cagescan_library_id}}}|{{{sample_species}}}}}|}}{{#ifexpr: {{#pos:{{{hg38bam_cs1}}}{{{mm10ctss_cs}}}|ttp}}| |
− | | | + | {{#switch: {{{sample_species}}} |
− | + | |Human (Homo sapiens) = {{FastaBamfileCTSS|HumanCAGEScan|Hg19|{{{hg19fasta_cs3prime}}}|{{{hg19fasta_cs5prime}}}|{{{hg19bam_cs}}}|{{{hg19ctss_cs}}}|Hg38|{{{hg38bam_cs}}}|{{{hg38ctss_cs}}}}} | |
− | | | + | |Mouse (Mus musculus) = {{FastaBamfileCTSS|HumanCAGEScan|Mm9|{{{mm9fasta_cs}}}||{{{mm9bam_cs}}}|{{{mm9ctss_cs}}}|Mm10|{{{mm10bam_cs}}}|{{{mm10ctss_cs}}}}} |
− | | | + | | |
− | + | }} | |
− | | | + | |}}{{#ifexpr:{{#pos:{{{HumanCAGEScanFiles}}}|ttp}}|{{FastaBamfileCTSSforCAGEScan|{{{HumanCAGEScanFiles}}}}} |
− | |- | + | |}}{{#if:{{#pos:{{{DRA_sample_Accession_RNASeq}}}|@|0}}|{{DRAAccessionNumbers|RNA-Seq|{{{DRA_sample_Accession_RNASeq}}}|{{{accession_numbers_RNASeq}}}|{{{rnaseq_library_id}}}|{{{sample_species}}}}}|}} |
− | + | {{#ifexpr:{{#pos:{{{RNASeqFiles}}}|ttp}}|{{FastaBamfileCTSSforCAGEScan|{{{RNASeqFiles}}}}} | |
− | | | + | |}}<br/> |
− | | | + | {{#if: {{#pos:{{{expression_enrichment_score}}}|chr}}| {{Fontsize|3|Relative expression to median (log10)}} |
− | ! | + | ---- |
− | + | {{Fontsize|3|Transcription factors with enriched expression in this sample}}{{nowrap|{{#info: Ranked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. }}}} | |
+ | <html><!-- tf enrich table: start--> | ||
+ | <script type="text/javascript"> | ||
+ | var species="</html>{{#var:species_temp}}<html>"; | ||
+ | var mm_data = new Array(); | ||
+ | var enrichment_scores_data = "</html>{{{expression_enrichment_score}}}<html>"; | ||
+ | var sub_content = enrichment_scores_data.split(";;"); | ||
− | + | $(document).ready(function() { | |
− | |||
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− | |||
− | + | for(i=0;i<sub_content.length;i++){ | |
− | + | var temp =sub_content[i]; | |
− | + | if(temp != null){ | |
− | + | if(temp.length>2){ | |
− | + | var sub_sub_content=sub_content[i].split("!"); | |
− | + | var built="FFCP_PHASE1:"+species+"::"+sub_sub_content[0]; | |
− | + | mm_data.push(sub_sub_content); | |
− | + | } | |
− | + | } | |
− | + | } | |
− | + | /*"sDom": '<"top"i>rt<"bottom"flp><"clear">' */ | |
− | |||
− | |||
− | |||
− | |||
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− | |||
− | + | $('#ffcp_tf_enrichscore').DataTable( { | |
− | + | data: mm_data, | |
− | + | dom: 'Blfrtip', | |
− | + | lengthMenu: [[10, 50, -1], [10, 50, "All"]], | |
− | + | buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'], | |
− | + | columnDefs: [{ targets: [1], visible: false}], | |
− | + | columns: [ | |
− | + | { title: "CAGE peaks" , | |
− | + | render: function ( data, type, row, meta ) { | |
− | + | var peak_loc = row[0]; | |
− | + | var peak_name = row[1]; | |
− | + | return "<a href=\"/5/sstar/"+"FFCP_PHASE1:"+species+"::"+peak_loc +"\">"+peak_name+"</a>"; | |
− | | | + | } |
− | + | }, | |
− | + | { title: "Log10(Relative expression over median)" }, | |
− | + | { title: "TPM" }, | |
− | + | { title: "TF." } | |
− | | | + | ], |
− | + | order: [[ 2, 'desc' ]] | |
− | + | } ); | |
− | + | }); | |
− | + | </script> | |
+ | <span id="tf_enrich_table_export_tool"></span> | ||
+ | <table cellpadding="0" cellspacing="0" border="0" id="ffcp_tf_enrichscore" class="stripe cell-border order-column compact"></table> | ||
+ | </html> | ||
+ | }} | ||
+ | {{#vardefine:isHumanOrMouse|{{#switch:{{{sample_species}}}|Human (Homo sapiens)=1|Mouse (Mus musculus)=1|0}}}} | ||
+ | {{#ifeq:{{#var:isHumanOrMouse}}|1|<br><br>{{Fontsize|3|Co-expression clusters with enriched expression in this sample}}{{#info:Ranked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters data]}}<html><script type="text/javascript"> | ||
+ | $(document).ready(function() { | ||
+ | if($('.relative-exp-of-coexp')[0]){ | ||
+ | $('.relative-exp-of-coexp').DataTable({ | ||
+ | dom: 'Blfrtip', | ||
+ | buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'], | ||
+ | lengthMenu: [[10, 50, -1], [10, 50, "All"]], | ||
+ | order: [[ 1, 'desc' ]] | ||
+ | }); | ||
+ | } | ||
+ | }); | ||
+ | </script></html>{{#switch:{{{sample_species}}}|Human (Homo sapiens)={{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$|{{#ask:[[Coexpression_dpi_cluster_scores_median_ffid::{{PAGENAME}}]][[Coexpression_dpi_cluster_scores_median_cnhs::{{#replace:$|CNhs|}}]]|?Coexpression_dpi_cluster_scores_median_value|intro=<table class="relative-exp-of-coexp stripe cell-border order-column compact"><html><thead></html><tr><th>Coexpression cluster</th><th>score</th></tr><html></thead><tbody></html>|outro=<html></tbody></html></table>|link=none|format=template|template=Coexpression_dpi_cluster_scores_median_in_ffsample|limit=5000|searchlabel=|default=No results for this sample}} | ||
+ | |<br><br>}} | ||
+ | |Mouse (Mus musculus)= | ||
+ | {{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$ | ||
+ | |<h3>$</h3>{{#ask:[[Coexpression_dpi_cluster_scores_median_ffid::{{PAGENAME}}]][[Coexpression_dpi_cluster_scores_median_cnhs::{{#replace:$|CNhs|}}]]|?=MCL coexpression id|?Coexpression_dpi_cluster_scores_median_value|format=ttable|class=relative-exp-of-coexp stripe cell-border order-column compact|searchlabel=}} | ||
+ | |<br><br> | ||
+ | }}}} | ||
+ | <br><br> | ||
+ | {{Fontsize|3|Repeat families with enriched expression in this sample}}{{nowrap|{{#info:<b>Summary:</b>Ranked list of repeat family expression in this sample relative to | ||
+ | the median expression in the FANTOM5 collection is shown. Value is log10 | ||
+ | transformed.<br><b>Analyst:</b>NA | ||
+ | <br><br>link to dataset.<br>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Repeat_expression data]}}}} | ||
+ | {{#if: {{#pos:{{{repeat_enrich_byfamily}}}|,}} | | ||
+ | <html><script type="text/javascript"> | ||
+ | $(document).ready(function() { | ||
+ | var repeat_enrich_byfamily_data = []; | ||
+ | var repeat_enrich_byfamily_repnames = [ | ||
+ | </html>{{#switch:{{{sample_species}}}|Human (Homo sapiens)=<html> | ||
+ | 'Alu','Alu,Alu','Alu,ERVL-MaLR','Alu,L1','Alu,L2','Alu,Low_complexity','Alu,MIR','Alu,hAT-Charlie','Alu,hAT-Tip100','Alu,rRNA','Alu,snRNA','CR1','CR1,CR1','DNA','DNA?','Deu','ERV','ERV1','ERV1,ERV1','ERV1,ERVL','ERV1,ERVL-MaLR','ERV1,MIR','ERV1,snRNA','ERVK','ERVK,rRNA','ERVL','ERVL,ERV1','ERVL,ERVL','ERVL,ERVL-MaLR','ERVL,hAT-Charlie','ERVL,snRNA','ERVL-MaLR','ERVL-MaLR,ERVL-MaLR','ERVL-MaLR,snRNA','ERVL?','Gypsy','Gypsy?','Helitron','L1','L1,ERV1','L1,ERVL','L1,ERVL-MaLR','L1,L1','L1,TcMar-Mariner','L1,TcMar-Tigger','L1,hAT-Charlie','L1,rRNA','L1,snRNA','L1?','L2','L2,ERV1','L2,ERVL-MaLR','L2,L2','L2,MIR','L2,hAT-Blackjack','L2,hAT-Charlie','LTR','Low_complexity','Low_complexity,Alu','Low_complexity,ERV1','Low_complexity,L2','Low_complexity,Low_complexity','Low_complexity,Low_complexity,Low_complexity','Low_complexity,snRNA','MIR','MIR,ERVL-MaLR','MIR,Low_complexity','MIR,MIR','Merlin','MuDR','NA','Other','PiggyBac','PiggyBac?','RNA','RNA,MIR','RTE','RTE,CR1','RTE-BovB','SINE','SINE?','Satellite','Satellite,ERVL','Simple_repeat','Simple_repeat,Alu','Simple_repeat,ERV1','Simple_repeat,ERVL','Simple_repeat,ERVL-MaLR','Simple_repeat,L1','Simple_repeat,L2','Simple_repeat,Low_complexity','Simple_repeat,Low_complexity,Low_complexity','Simple_repeat,MIR','Simple_repeat,Other','Simple_repeat,Simple_repeat','Simple_repeat,Simple_repeat,Low_complexity','Simple_repeat,Simple_repeat,Simple_repeat','Simple_repeat,TcMar-Tigger','Simple_repeat,Unknown','Simple_repeat,hAT-Charlie','Simple_repeat,hAT-Tip100','Simple_repeat,scRNA','Simple_repeat,snRNA','TcMar','TcMar-Mariner','TcMar-Tc2','TcMar-Tc2,ERV1','TcMar-Tigger','TcMar-Tigger,TcMar-Tigger','TcMar-Tigger,snRNA','TcMar?','Unknown','Unknown?','acro','centr','hAT','hAT-Blackjack','hAT-Charlie','hAT-Charlie,ERVL-MaLR','hAT-Charlie,MIR','hAT-Charlie,hAT-Charlie','hAT-Charlie,snRNA','hAT-Tip100','hAT?','rRNA','rRNA,rRNA','scRNA','scRNA,L1','snRNA','srpRNA','tRNA','telo' | ||
+ | </html>|Mouse (Mus musculus)=<html> | ||
+ | 'AcHobo','Alu','Alu,B4','Alu,B4,ERVL','Alu,ERVK','Alu,ERVL','Alu,L1','B2','B2,B4','B4','B4,Alu','B4,Low_complexity','CR1','ERV1','ERV1,ERVK','ERVK','ERVK,ERVK','ERVL','ERVL,Alu','ERVL,ERVK','ERVL,MaLR','ERVL?','Genie?','Gypsy','Gypsy?','Helitron','ID','ID,Satellite','L1','L1,ERVK','L1,L1','L1,snRNA','L1,tRNA','L2','L2,ERV1','L2,MaLR','LTR','Low_complexity','Low_complexity,Alu','Low_complexity,Low_complexity','Low_complexity,Low_complexity,Low_complexity','Low_complexity,MIR','Low_complexity,Tip100','Low_complexity,snRNA','MER1_type','MER1_type,B4','MER1_type?','MER2_type','MIR','MIR,MIR','MIR,MaLR','MaLR','MaLR,Alu','MaLR,ERV1','MaLR,ERVL','MaLR,MaLR','MuDR','NA','Other','PiggyBac','RNA','RTE','SINE','Satellite','Satellite,Satellite','Simple_repeat','Simple_repeat,Alu','Simple_repeat,Alu,B4','Simple_repeat,B2','Simple_repeat,B4','Simple_repeat,ERVK','Simple_repeat,L1','Simple_repeat,Low_complexity','Simple_repeat,Low_complexity,Low_complexity','Simple_repeat,MIR','Simple_repeat,MaLR','Simple_repeat,Simple_repeat','Simple_repeat,Simple_repeat,Low_complexity','Simple_repeat,rRNA','Tc2','TcMar','Tigger','Tip100','Unknown','hAT','hAT?','rRNA','rRNA,B4','rRNA,ERVK','scRNA','scRNA,B4','scRNA,Satellite','snRNA','tRNA' | ||
+ | </html>}}<html> | ||
+ | ]; | ||
+ | var repeat_enrich_byfamily_values = [</html>{{{repeat_enrich_byfamily}}}<html>]; | ||
+ | for(i1=0;i1<repeat_enrich_byfamily_repnames.length;i1++){ | ||
+ | repeat_enrich_byfamily_data.push([repeat_enrich_byfamily_repnames[i1],repeat_enrich_byfamily_values[i1]]); | ||
+ | } | ||
+ | $('#repeat_enrich_byfamily_table').DataTable({ | ||
+ | data: repeat_enrich_byfamily_data, | ||
+ | dom: 'Blfrtip', | ||
+ | buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'], | ||
+ | lengthMenu: [[5, 50, -1], [5, 50, "All"]], | ||
+ | columns: [ | ||
+ | { title: "Repeat family" }, | ||
+ | { title: "Log10(Relative expression over median)" , | ||
+ | render: function ( data, type, row, meta ) { | ||
+ | var num = row[1]; | ||
+ | var numb = new Number(num); | ||
+ | return numb.toFixed(2); | ||
+ | } | ||
+ | } | ||
+ | ], | ||
+ | order: [[ 1, 'desc' ]] | ||
+ | }); | ||
+ | }); | ||
+ | </script> | ||
+ | <span id="repeat_enrich_byfamily_table_export_tool"></span> | ||
+ | <table id="repeat_enrich_byfamily_table" class="stripe cell-border order-column compact"></table><br> | ||
+ | </html> | ||
+ | |no result for this sample | ||
+ | }} | ||
− | {{{ | + | <br> |
+ | {{Fontsize|3|TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample}} | ||
+ | ---- | ||
+ | {{Fontsize|3|JASPAR motifs}}{{#info:<b>Summary:</b>Association of JASPAR motif to the promoter expression in this | ||
+ | sample. Pearson's correlation between the number of TFBSs estimated by | ||
+ | using the position-weight matrix for each promoter and its expression is | ||
+ | expressed as Z-score by taking the ones based on random position-weight | ||
+ | matrix, and the tail probability of the normal distribution corresponding | ||
+ | to the Z-score is taken as the resulting P-value. Lower P-value indicates | ||
+ | more (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br> | ||
+ | <br><br>link to dataset.<br>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/jaspar_Significance_of_the_correlation_with_CAGE_expression data]}}<br> | ||
+ | {{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$ | ||
+ | |library id: $<span id="related_jaspar_table_export_tool"></span>{{#ask:[[jaspar_motifs_sample_pval_ffid::{{PAGENAME}}{{#replace:$|CNhs|_}}]]|?=Jaspar motif|?=Logo|?jaspar_motifs_sample_pval_pval=P-value|format=ttable|limit=1100|searchlabel=|class=jaspar_motif_pval stripe cell-border order-column compact|searchlabel=|default=This sample isn't target for the analysis}} | ||
+ | |<br> | ||
+ | }} | ||
+ | <br><br> | ||
+ | {{Fontsize|3|FANTOM5 phase1 novel unique motifs}}{{#info:<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in | ||
+ | 169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br> | ||
+ | <br><br>link to dataset.<br>[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_Significance_of_the_correlation_with_CAGE_expression data]}}<br> | ||
+ | {{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$ | ||
+ | |library id: $<span id="related_novel_table_export_tool"></span>{{#ask:[[novel_motifs_sample_pval_ffid::{{PAGENAME}}{{#replace:$|CNhs|_}}]]|?=Novel motif|?=Logo|?novel_motifs_sample_pval_pval=P-value|format=ttable|limit=1100|searchlabel=|class=novel_motif_pval stripe cell-border order-column compact|searchlabel=|default=This sample isn't target for the analysis}} | ||
+ | |<br> | ||
+ | }} | ||
+ | <br><br> | ||
+ | {{Fontsize|3|de novo motifs identified by HOMER in promoters active in this sample}}{{#info:<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br>}} | ||
+ | {{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$ | ||
+ | |library id: ${{#outerfile_existance:/5/sstar/Homer_de_novo_Motif_Results/$/homerResults.html | ||
+ | |<div id="homer_denovo_table_export_tool"></div><br>{{#homer_list:Homer_de_novo_Motif_Results/$/homerResults.html|homerResults!<TABLE cellpadding="2" cellspacing="0">!</div></TD></TR>!</TABLE>!Homer de novo Motif Results|/5/sstar/Homer_de_novo_Motif_Results/$/homerResults!<table class=homer-table><thead>!</div></TD></TR></thead><tbody>!</tbody></TABLE>|!}} | ||
+ | }} | ||
+ | |<br> | ||
+ | }}<br> | ||
+ | <html> | ||
+ | <script type="text/javascript"> | ||
+ | $(document).ready(function() { | ||
+ | if($('.jaspar_motif_pval')[0]){ | ||
+ | $('.jaspar_motif_pval').DataTable({ | ||
+ | dom: 'Blfrtip', | ||
+ | buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'], | ||
+ | lengthMenu: [[5, 50, -1], [5, 50, "All"]], | ||
+ | columnDefs: [ | ||
+ | { targets: 0, orderable: false}, | ||
+ | { targets: 1, orderable: false, width: "50pt", className: "bgwhite"} | ||
+ | ], | ||
+ | columns: [ | ||
+ | { title: "Jaspar motif" }, | ||
+ | { title: "Logo", | ||
+ | render: function ( data, type, row, meta ) { | ||
+ | return "<img src=\"/5/sstar/seqlogo/jaspar/" + $(row[0]).text() + ".png\" width =\"80\" height = \"20\">"; | ||
+ | } | ||
+ | }, | ||
+ | { title: "p-value", | ||
+ | render: function ( data, type, row, meta ) { | ||
+ | var num=row[2]; | ||
+ | return exp_converter(num,2,"e") ; | ||
+ | } | ||
+ | } | ||
+ | ], | ||
+ | order: [[ 2, 'asc' ]] | ||
+ | }); | ||
+ | } | ||
+ | }); | ||
+ | </script> | ||
+ | </html> | ||
+ | <html> | ||
+ | <script type="text/javascript"> | ||
+ | $(document).ready(function() { | ||
+ | if($('.novel_motif_pval')[0]){ | ||
+ | $('.novel_motif_pval').DataTable({ | ||
+ | dom: 'Blfrtip', | ||
+ | buttons: ['copyHtml5', 'excelHtml5', 'csvHtml5', 'pdfHtml5'], | ||
+ | lengthMenu: [[5, 50, -1], [5, 50, "All"]], | ||
+ | columnDefs: [ | ||
+ | { targets: 0, orderable: false}, | ||
+ | { targets: 1, orderable: false, width: "50pt", className: "bgwhite"} | ||
+ | ], | ||
+ | columns: [ | ||
+ | { title: "Novel motif" }, | ||
+ | { title: "Logo", | ||
+ | render: function ( data, type, row, meta ) { | ||
+ | return "<img src=\"/5/sstar/seqlogo/novel/" + $(row[0]).text() + ".png\" width =\"80\" height = \"20\">"; | ||
+ | } | ||
+ | }, | ||
+ | { title: "p-value", | ||
+ | render: function ( data, type, row, meta ) { | ||
+ | var num=row[2]; | ||
+ | return exp_converter(num,2,"e") ; | ||
+ | } | ||
+ | } | ||
+ | ], | ||
+ | order: [[ 2, 'asc' ]] | ||
+ | }); | ||
− | + | } | |
− | + | }); | |
− | + | </script> | |
− | + | </html> | |
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
− | == | + | <html> |
− | {{#if: {{{ | + | <style type="text/css"> |
− | {{# | + | .white { background-color: white} |
− | {{#if: {{{ | + | table.homer-table td { padding: 1px } |
+ | </style> | ||
+ | <script type="text/javascript" language="javascript" src="/5/sstar/rb_js/datatables/media/js/dataTables.Percentage.js"></script> | ||
+ | </html> | ||
+ | <br>|}}<!-- end of if(isHumanOrMouse) --> | ||
+ | {{Fontsize|3|FANTOM5 (FF) ontology }} | ||
+ | ---- | ||
+ | {{Fontsize|3|Direct parent terms}} | ||
+ | {{#if: {{{is_a}}} | | ||
+ | <div style="width:25%; float:left;"> | ||
+ | '''is_a relathionship'''<br>{{#arraymap:{{{is_a}}}|;;|$| | ||
+ | {{#set:is_a=$}}{{#ifexist:$|[[$|$ {{#show:$|?name}}]]|$}}|<br>}} | ||
+ | </div> | ||
+ | |}} | ||
+ | {{#if: {{{part_of}}} | | ||
+ | <div style="width:25%; float:left;"> | ||
+ | '''part_of relathionship'''<br>{{#arraymap:{{{part_of}}}|;;|$| | ||
+ | {{#set:part_of=$}}{{#ifexist:$|[[$|$ {{#show:$|?name}}]]|$}}|<br>}} | ||
+ | </div> | ||
+ | |}} | ||
+ | {{#if: {{{has_quality}}} | | ||
+ | <div style="width:25%; float:left;"> | ||
+ | '''has_quality relathionship'''<br>{{#arraymap:{{{has_quality}}}|;;|$| | ||
+ | {{#set:has_quality=$}}{{#ifexist:$|[[$|$ {{#show:$|?name}}]]|$}}|<br>}} | ||
+ | </div> | ||
+ | |}} | ||
+ | <div style="clear:both;"></div> | ||
− | {{#arraymap:{{{ancestors_in_cell_lineage_facet | + | {{Fontsize|3|Ancestor terms (non development)}}{{#info:<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji |
− | {{#arraymap:{{{ancestors_in_disease_facet | + | <br><br>link to source data<br> |
− | {{#arraymap:{{{ancestors_in_anatomy_facet | + | [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Ontology/ontology_mapping/ data] |
+ | }}<br> | ||
+ | {{#if: {{{ancestors_in_cell_lineage_facet}}} | | ||
+ | <div style="width:25%; float:left;"> | ||
+ | <b>CL: Cell type</b><br> | ||
+ | {{#ifeq: 0|{{#expr:{{#if:{{#pos:{{{ancestors_in_cell_lineage_facet}}}|:|0}}|1|0}}}}|NA|{{#arraymap:{{{ancestors_in_cell_lineage_facet}}}|,|$|{{#set:ancestors_in_cell_lineage_facet=$}}{{#ask:[[id::$]]|?name=|format=list}}|<br>}} }} | ||
+ | </div> | ||
+ | }}{{#if: {{{ancestors_in_disease_facet}}} | | ||
+ | <div style="width:25%; float:left;"> | ||
+ | <b>DOID: Disease</b><br> | ||
+ | {{#ifeq: 0|{{#expr:{{#if:{{#pos:{{{ancestors_in_disease_facet}}}|:|0}}|1|0}}}}|NA|{{#arraymap:{{{ancestors_in_disease_facet}}}|,|$|{{#set:ancestors_in_disease_facet=$}}{{#ask:[[id::$]]|?name=|format=list}}|<br>}} }} | ||
+ | </div> | ||
+ | }}{{#if: {{{ancestors_in_anatomy_facet}}} | | ||
+ | <div style="width:25%; float:left;"> | ||
+ | <b>UBERON: Anatomy</b><br> | ||
+ | {{#ifeq: 0|{{#expr:{{#if:{{#pos:{{{ancestors_in_anatomy_facet}}}|:|0}}|1|0}}}}|NA|{{#arraymap:{{{ancestors_in_anatomy_facet}}}|,|$|{{#set:ancestors_in_anatomy_facet=$}}{{#ask:[[id::$]]|?name=|format=list}}|<br>}} }} | ||
+ | </div> | ||
+ | }}{{#if: {{{ancestors_in_ff_facet}}} | | ||
+ | <div style="width:25%; float:left;"> | ||
+ | <b>FF: FANTOM5</b><br> | ||
+ | {{#ifeq: 0|{{#expr:{{#if:{{#pos:{{{ancestors_in_ff_facet}}}|:|0}}|1|0}}}}|NA|{{#arraymap:{{{ancestors_in_ff_facet}}}|,|$|{{#set:ancestors_in_ff_facet=$}}{{#ask:[[id::$]]|?name=|format=list}}|<br>}} }} | ||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
</div> | </div> | ||
+ | }} | ||
+ | <div style="clear:both;"></div> | ||
+ | |||
+ | {{Fontsize|3|Ancestor terms (development)}}{{#info:<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br> | ||
+ | <b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br> | ||
+ | [http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Ontology/ontology_mapping/ data] | ||
+ | }} | ||
+ | <br> | ||
+ | {{#ifeq: 0|{{#expr:{{#if:{{#pos:{{{ffid_belonging_in_development}}}|:|0}}|1|0}}}}|NA|{{#arraymap:{{{ffid_belonging_in_development}}}|,|$|{{#ifexist:$|{{#set:ffid_belonging_in_development=$}}[[$]] ({{#show:$|?name}})}}|<br>}} }} | ||
+ | <br><br> | ||
+ | {{#if:{{#pos:{{{DRA_sample_Accession}}}|@|0}}| | ||
+ | {{#set:sample_category={{{sample_category}}}}} | ||
+ | {{#arraymap:{{{library_id}}}|!|$ | ||
+ | |{{#set:Library accession number=$}} | ||
+ | }} | ||
+ | |||
+ | {{#arraydefine:accession_numbers_array|{{{accession_numbers}}}|!}}{{#loop: k | ||
+ | | 0 | ||
+ | | {{#arraysize:accession_numbers_array}} | ||
+ | | <nowiki/> | ||
+ | {{#vardefine:exp_met|{{#explode:{{#arrayindex:accession_numbers_array|{{#var:k}}}}|;|0}}}} | ||
+ | {{#if:{{#var:exp_met}}|{{#set:Experiment method={{#var:exp_met}}}}|}} | ||
+ | {{#vardefine:lib_exp|{{#explode:{{#arrayindex:accession_numbers_array|{{#var:k}}}}|;|1}}}} | ||
+ | {{#if:{{#var:lib_exp}}|{{#set:Experiment accession number={{#var:lib_exp}}}}|}} | ||
+ | {{#vardefine:lib_run|{{#explode:{{#arrayindex:accession_numbers_array|{{#var:k}}}}|;|2}}}} | ||
+ | {{#if:{{#var:lib_run}}|{{#set:Run accession number={{#var:lib_run}}}}|}} | ||
+ | {{#vardefine:lib_bam|{{#explode:{{#arrayindex:accession_numbers_array|{{#var:k}}}}|;|3}}}} | ||
+ | {{#if:{{#var:lib_bam}}|{{#set:Bam accession number={{#var:lib_bam}}|BAM}}|}} | ||
+ | {{#vardefine:lib_ctss|{{#explode:{{#arrayindex:accession_numbers_array|{{#var:k}}}}|;|4}}}} | ||
+ | {{#if:{{#var:lib_ctss}}|{{#set:CTSS accession number={{#var:lib_ctss}}}}|}} | ||
+ | }} | ||
+ | |}} | ||
+ | |||
+ | |||
+ | {{#set:sample_category={{{sample_category}}}}} | ||
+ | {{#set:profile_hcage={{{profile_hcage}}}}} | ||
+ | {{#set:profile_rnaseq={{{profile_rnaseq}}}}} | ||
+ | {{#set:profile_srnaseq={{{profile_srnaseq}}}}} | ||
+ | {{#set:profile_cagescan={{{profile_cagescan}}}}} | ||
+ | {{#set:sample_strain={{{sample_strain}}}}} | ||
+ | {{#set:sample_tissue={{{sample_tissue}}}}} | ||
+ | {{#set:sample_dev_stage={{{sample_dev_stage}}}}} | ||
+ | {{#set:sample_sex={{{sample_sex}}}}} | ||
+ | {{#set:sample_age={{{sample_age}}}}} | ||
+ | {{#set:sample_ethnicity={{{sample_ethnicity}}}}} | ||
+ | {{#set:sample_cell_type={{{sample_cell_type}}}}} | ||
+ | {{#set:sample_cell_line={{{sample_cell_line}}}}} | ||
+ | {{#set:sample_collaboration={{{sample_collaboration}}}}} | ||
+ | {{#set:sample_experimental_condition={{{sample_experimental_condition}}}}} | ||
+ | {{#set:sample_disease={{{sample_disease}}}}} | ||
+ | {{#set:sample_cell_lot={{{sample_cell_lot}}}}} | ||
+ | {{#set:sample_cell_catalog={{{sample_cell_catalog}}}}} | ||
+ | {{#set:sample_company={{{sample_company}}}}} | ||
+ | {{#set:sample_donor(cell lot)={{{sample_donor(cell lot)}}}}} | ||
+ | {{#set:sample_note={{{sample_note}}}}} | ||
+ | {{#set:sample_id={{{sample_id}}}}} | ||
+ | {{#set:rna_tube_id={{{rna_tube_id}}}}} | ||
+ | {{#set:rna_box={{{rna_box}}}}} | ||
+ | {{#set:rna_position={{{rna_position}}}}} | ||
+ | {{#set:rna_lot_number={{{rna_lot_number}}}}} | ||
+ | {{#set:rna_catalog_number={{{rna_catalog_number}}}}} | ||
+ | {{#set:rna_rin={{{rna_rin}}}}} | ||
+ | {{#set:rna_od260/230={{{rna_od260/230}}}}} | ||
+ | {{#set:rna_od260/280={{{rna_od260/280}}}}} | ||
+ | {{#set:rna_sample_type={{{rna_sample_type}}}}} | ||
+ | {{#set:rna_extraction_protocol={{{rna_extraction_protocol}}}}} | ||
+ | {{#set:rna_weight_ug={{{rna_weight_ug}}}}} | ||
+ | {{#set:rna_concentration={{{rna_concentration}}}}} | ||
+ | {{#if:{{{timecourse}}}|{{#arraymap:{{{timecourse|}}}|,|$| {{#set:timecourse=$}}}}|}} | ||
+ | {{#set:donor={{{donor}}}}} | ||
+ | {{#set:time={{{time}}}}} | ||
+ | {{#switch:{{{datafreeze_phase}}}|1={{#set:datafreeze_phase=1}}|2={{#set:datafreeze_phase=2}}|{{#set:datafreeze_phase=-1}}}} | ||
+ | {{#arraymap:{{#explode:{{{profile_hcage|}}}|,|0}}|&|$ | ||
+ | |{{#set:sample_seq_library_id=$}} | ||
+ | }} | ||
+ | {{#set:sample_timecourse={{{sample_timecourse|}}}}} | ||
[[Category:FF_Ontology]] | [[Category:FF_Ontology]] | ||
+ | [[Category:FF_Samples]] | ||
+ | |||
+ | <html> | ||
+ | <script type="text/javascript"> | ||
+ | $(document).ready(function() { | ||
+ | if($('.homer-table')[0]){ | ||
+ | var homer_denovo_table = $('.homer-table').dataTable({ | ||
+ | "bPaginate": true, | ||
+ | "bInfo": true, | ||
+ | "bScrollCollapse": true, | ||
+ | "iDisplayLength": 5, | ||
+ | "aLengthMenu": [[5,50,-1], [5,50,"All"]], | ||
+ | "aaSorting": [], | ||
+ | "aoColumnDefs": [{ "sType": "numeric", "sWidth": "100px", "aTargets": [2]}, {"sType": "percent", "aTargets": [ 3, 4] }, { "bSortable": false, "aTargets": [ 0, 1, 5] }] | ||
+ | }); | ||
+ | |||
+ | var homer_denovo_table_tool = new TableTools(homer_denovo_table, {"sSwfPath": "/5/sstar/rb_js/datatables/extras/TableTools/media/swf/copy_csv_xls_pdf.swf", "aButtons": [ {"sExtends": "copy", "mColumns": "visible"},{"sExtends": "csv", "mColumns": "visible"},{"sExtends": "pdf", "mColumns": "visible"} ]}); | ||
+ | |||
+ | $('#homer_denovo_table_export_tool').before(homer_denovo_table_tool.dom.container ); | ||
+ | } | ||
+ | }); | ||
+ | </script> | ||
+ | </html> |
Latest revision as of 07:52, 23 May 2019
Name: | {{{name}}} |
---|---|
Species: | {{{sample_species}}} |
Library ID: | {{{library_id}}} |
Sample type: | {{{sample_category}}} |
Genomic View: |
Additional information | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample information
RNA information
|
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
{{{is_a}}}
part_of relathionship
{{{part_of}}}
has_quality relathionship
{{{has_quality}}}
Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji
link to source data
data
CL: Cell type
NA
DOID: Disease
NA
UBERON: Anatomy
NA
FF: FANTOM5
NA
Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji
link to source data
data
NA